RetrogeneDB ID: retro_ptro_515

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:99216817..99217159(-)
• Located in intron of: ENSPTRG00000002832

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EBAG9
• Ensembl ID: ENSPTRG00000020513
• Aliases: None
• Description: None

Sequence

>retro_ptro_515
ATGGCCGTAACACAGGTCCAGTTATTTTGAGTTTATACTTGCCTAGCAACCATATTCTCATTCCTCAAAATGATGAGTAT
GAAGATCTGTCCAAGGACAGAAATTAAGTTGGGGTCCAAGTAACTTTGCCAATTGCAGTTAATTATTCATCAGTTCCTAA
ACAGACAGATGTTGAAGAGTGGACTTCTTAGAATGAGGATGCACCCACAGGTGTAAAGACCGAGAGTGAGAATGGAATGA
GGCAGTACAACAGAACACTTTACAACAACTGGAACCGACTATTTTAAGGATGTGACACCAACTGTAAGGAAAACTCAGAA
AATTGTTACTGAGAAGAGACAA

Alignment

ORF - retro_ptro_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.8 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAITQFRLFKFCTCLATVFSFLKRL-ICRSGRGRKLS-GDQITLPTTVDYSSVPKQTDVEEWTSWDEDAP
          MA.TQ..LF...TCLAT.FSFLK.....RS..G.KLS.G.Q.TLP..V.YSSVPKQTDVEEWTS..EDAP
Retrocopy MAVTQVQLF*VYTCLATIFSFLKMM>V*RSVQGQKLS>GVQVTLPIAVNYSSVPKQTDVEEWTS*NEDAP

Parental  TSVKIEGGNG-NVATQQNSLEQLEP-DYFKDMTPTIRKTQKIVIKKRE
          T.VK.E..NG.N.A.QQN.L.QLEP.DYFKD.TPT.RKTQKIV..KR.
Retrocopy TGVKTESENG<NEAVQQNTLQQLEP<DYFKDVTPTVRKTQKIVTEKRQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.05 RPM	10.44 RPM
SRP007412_cerebellum	0.22 RPM	14.30 RPM
SRP007412_heart	0.03 RPM	9.36 RPM
SRP007412_kidney	0.03 RPM	15.48 RPM
SRP007412_liver	0.07 RPM	9.43 RPM
SRP007412_testis	0.00 RPM	43.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_515 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_515 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_622

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007465	2 retrocopies	retro_dnov_1014, retro_dnov_2449,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Pongo abelii	ENSPPYG00000018824	1 retrocopy	retro_pabe_622,
Pan troglodytes	ENSPTRG00000020513	1 retrocopy	retro_ptro_515 ,